def index_dir():
from gimmemotifs.genome_index import GenomeIndex
test_index_dir = 'tests/data/index/'
g = GenomeIndex()
g.create_index('tests/data/genome/', test_index_dir)
return test_index_dir
def index(args):
if not os.path.exists(args.indexdir):
print "Index_dir %s does not exist!" % (args.indexdir)
sys.exit(1)
fasta_dir = args.fastadir
index_dir = os.path.join(args.indexdir, args.indexname)
g = GenomeIndex()
g.create_index(fasta_dir, index_dir)
# Create genome FASTA file for use with bedtools
with open(os.path.join(index_dir, "genome.fa"), 'w') as out:
for f in find_by_ext(fasta_dir, FASTA_EXT):
for line in open(f):
out.write(line)
test_chr = g.get_chromosomes()[0]
tmp = NamedTemporaryFile()
tmp.write("{}\t1\t2\n".format(test_chr))
tmp.flush()
b = pybedtools.BedTool(tmp.name)
try:
b.nucleotide_content(fi=os.path.join(index_dir, "genome.fa"))
except pybedtools.helpers.BEDToolsError as e:
if str(e).find("generating") == -1:
raise
def index_dir():
from gimmemotifs.genome_index import GenomeIndex
test_index_dir = 'tests/data/index/'
g = GenomeIndex()
g.create_index('tests/data/genome/', test_index_dir)
return test_index_dir
def index(args):
if not os.path.exists(args.indexdir):
print "Index_dir %s does not exist!" % (args.indexdir)
sys.exit(1)
fasta_dir = args.fastadir
index_dir = os.path.join(args.indexdir, args.indexname)
g = GenomeIndex()
g.create_index(fasta_dir, index_dir)
create_bedtools_fa(index_dir, fasta_dir)
def test2_as_fasta(self):
""" convert bed, regions, etc to Fasta """
tmpdir = mkdtemp()
g = GenomeIndex()
g.create_index(self.genome_dir, tmpdir)
fafile = os.path.join(self.datadir, "test.fa")
fa = Fasta(fafile)
bedfile = os.path.join(self.datadir, "test.bed")
regionfile = os.path.join(self.datadir, "test.txt")
regions = [l.strip() for l in open(regionfile)]
self.assertTrue(isinstance(as_fasta(fa), Fasta))
self.assertTrue(isinstance(as_fasta(fafile), Fasta))
self.assertTrue(isinstance(as_fasta(bedfile, tmpdir), Fasta))
self.assertTrue(isinstance(as_fasta(regionfile, tmpdir), Fasta))
self.assertTrue(isinstance(as_fasta(regions, tmpdir), Fasta))
with self.assertRaises(ValueError):
as_fasta(bedfile)
rmtree(tmpdir)
def test2_as_fasta(self):
""" convert bed, regions, etc to Fasta """
tmpdir = mkdtemp()
g = GenomeIndex()
g.create_index(self.genome_dir, tmpdir)
fafile = os.path.join(self.datadir, "test.fa")
fa = Fasta(fafile)
bedfile = os.path.join(self.datadir, "test.bed")
regionfile = os.path.join(self.datadir, "test.txt")
regions = [l.strip() for l in open(regionfile)]
self.assertTrue(isinstance(as_fasta(fa), Fasta))
self.assertTrue(isinstance(as_fasta(fafile), Fasta))
self.assertTrue(isinstance(as_fasta(bedfile, tmpdir), Fasta))
self.assertTrue(isinstance(as_fasta(regionfile, tmpdir), Fasta))
self.assertTrue(isinstance(as_fasta(regions, tmpdir), Fasta))
with self.assertRaises(ValueError):
as_fasta(bedfile)
rmtree(tmpdir)
def genome(args):
config = MotifConfig()
if not os.path.exists(args.indexdir):
print "Index_dir %s does not exist!" % (args.indexdir)
sys.exit(1)
if not os.path.exists(args.fastadir):
print "FASTA dir %s does not exist!" % (args.fastadir)
sys.exit(1)
pred_bin = "genePredToBed"
pred = find_executable(pred_bin)
if not pred:
sys.stderr.write("{} not found in path!\n".format(pred_bin))
sys.exit(1)
fastadir = args.fastadir
genomebuild = args.genomebuild
genome_dir = os.path.join(fastadir, genomebuild)
index_dir = os.path.join(args.indexdir, args.genomebuild)
# Check for rights to write to directory
if not os.path.exists(genome_dir):
try:
os.mkdir(genome_dir)
except:
sys.stderr.write("Could not create genome dir {}\n".format(genome_dir))
sys.exit(1)
# Download gene file based on URL + genomebuild
gene_file = os.path.join(config.get_gene_dir(), "%s.bed" % genomebuild)
tmp = NamedTemporaryFile(delete=False, suffix=".gz")
anno = []
f = urllib2.urlopen(UCSC_GENE_URL.format(genomebuild))
p = re.compile(r'\w+.Gene.txt.gz')
for line in f.readlines():
m = p.search(line)
if m:
anno.append(m.group(0))
sys.stderr.write("Retrieving gene annotation for {}\n".format(genomebuild))
url = ""
for a in ANNOS:
if a in anno:
url = UCSC_GENE_URL.format(genomebuild) + a
break
if url:
urllib.urlretrieve(
url,
tmp.name
)
sp.call("zcat {} | cut -f2-11 | {} /dev/stdin {}".format(tmp.name, pred, gene_file), shell=True)
else:
sys.stderr.write("No annotation found!")
# download genome based on URL + genomebuild
sys.stderr.write("Downloading {} genome\n".format(genomebuild))
for genome_url in [UCSC_GENOME_URL, ALT_UCSC_GENOME_URL]:
remote = genome_url.format(genomebuild)
genome_fa = os.path.join(
genome_dir,
os.path.split(remote)[-1]
)
sys.stderr.write("Trying to download {}\n".format(genome_url.format(genomebuild)))
urllib.urlretrieve(
genome_url.format(genomebuild),
genome_fa
)
if not check_genome_file(genome_fa):
continue
break
if not check_genome_file(genome_fa):
sys.stderr.write("Failed to download genome\n")
sys.exit(1)
sys.stderr.write("Unpacking\n")
if genome_fa.endswith("tar.gz"):
cmd = "tar -C {0} -xvzf {1} && rm {1}".format(genome_dir, genome_fa)
else:
cmd = "gunzip {0} && rm {0}".format(genome_fa)
sp.call(cmd, shell=True, cwd=genome_dir)
fa_files = glob("{}/*.fa".format(genome_dir))
if len(fa_files) == 1:
f = Fasta(fa_files[0])
for n,s in f.items():
with open("{}/{}.fa".format(n)) as f:
f.write("{}\n{}\n".format(n,s))
os.unlink(fa_files[0])
sys.stderr.write("Creating index\n")
g = GenomeIndex()
g = g.create_index(genome_dir, index_dir)
